[phenixbb] Weird R-free discrepancy.

Yuri yuri.pompeu at ufl.edu
Sat May 21 19:55:55 PDT 2011


I was working on a model for  at 1.9 A using the previous phenix 
release (650). I was almost finished r-free was 0.197. I installed the 
newest release and refined again and my r-free went up to 0.228!!.
The values for bsol and ksol look significantly different. I do not 
understand where the biggest difference is coming from...
Below I pasted part of the .log files. Old and new, respectively.

=============================== refinement start 
==============================


    ----------structure factors based statistics (before 
refinement)----------


                          ----------X-ray data----------

|--(resolution: 1.90 - 28.74 A; n_refl. = 
32203)------------------------------|
|                                                                       
      |
| r_work= 0.1747   r_free= 0.1967   ksol= 0.40   Bsol= 39.70   scale= 
0.064   |
|                                                                       
      |
| overall anisotropic scale matrix (Cartesian basis; 
B11,B22,B33,B12,B13,B23):|
| (-1.65,-1.65,3.31,-0.00,0.00,0.00); trace/3= -0.00                    
      |
|                                                                       
      |
| maximum likelihood estimate for coordinate error:   0.21 A            
      |
| x-ray target function (ml) for work reflections: 2.567485             
      |


=============================== refinement start 
==============================


    ----------structure factors based statistics (before 
refinement)----------


                          ----------X-ray data----------

|--(resolution: 1.90 - 28.74 A; n_refl. = 
34277)------------------------------|
|                                                                       
      |
| r_work= 0.1911   r_free= 0.2279   ksol= 0.40   Bsol= 59.62   scale= 
0.063   |
|                                                                       
      |
| overall anisotropic scale matrix (Cartesian basis; 
B11,B22,B33,B12,B13,B23):|
| (-1.73,-1.73,3.47,0.00,0.00,-0.00); trace/3= 0.00                     
      |
|                                                                       
      |
| maximum likelihood estimate for coordinate error:   0.55 A            
      |
| x-ray target function (ml) for work reflections: 2.591014             
      |
|-----------------------------------------------------------------------------|


-- 
Yuri Pompeu


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